I don't think energy shields ever affected missiles in the first place. The energy shield nerf just made mantas not benefit from it (which I don't feel was necessary tbh, as it replaces the very powerful cooldown launchbay upgrade. Eldar squadrons are actually more resilient now with their free dodge, at least the bomber ones. Tau fighters are still the best with this upgrade)

While I think the FIVE anti-ordenance attacks on the Manta are way too much, the 2 hp was not too much balance wise I think since they are the only long range weapon the Tau currently have beside the railgun cheese experiment.

Barracudas having 2 HP is just silly. They are one of the weakest and tiniest fighters around. If the upgrade gave just the Mantas 2 Hp than it would be more accurate.Or rather I would give it 2 hp to mantas, and split mantas into 3 bombers like other races got it with fighter cover. Since they are like the third smallest bomber in game.

So if I were to categorify them, the fightabomma-barracuda-Stormhawk-Thunderhawk and eldar craft are all hard to hit due to their size and/or manoeverability.By all and every means though, both Mantas and Thunderhawks should be not be more durable than bombers 3-4 times their size.

Though Seeker missiles upgrade is just plain wrong. Check these tabletop stats.

Seeker missile: S8 Ap3 Turbo-laser: S:D Ap2

So we are saying that Seeker missiles deal more damage than the turbolasers that imperial-made craft use for point defence? Sounds utterly ludicrous.